Fix Codex skill injection to use ~/.codex/skills/ instead of cwd

The Codex adapter was the only one injecting skills into
<cwd>/.agents/skills/, polluting the project's git repo. All other
adapters (Gemini, Cursor, etc.) use a home-based directory. This
changes the Codex adapter to inject into ~/.codex/skills/ (resolved
via resolveSharedCodexHomeDir) to match the established pattern.

Co-Authored-By: Paperclip <noreply@paperclip.ing>

packages/adapters/codex-local/src/index.ts

@@ -42,7 +42,7 @@ Notes:
 - Prompts are piped via stdin (Codex receives "-" prompt argument).
 - If instructionsFilePath is configured, Paperclip prepends that file's contents to the stdin prompt on every run.
 - Codex exec automatically applies repo-scoped AGENTS.md instructions from the active workspace. Paperclip cannot suppress that discovery in exec mode, so repo AGENTS.md files may still apply even when you only configured an explicit instructionsFilePath.
-- Paperclip injects desired local skills into the active workspace's ".agents/skills" directory at execution time so Codex can discover "$paperclip" and related skills without coupling them to the user's login home.
+- Paperclip injects desired local skills into ~/.codex/skills/ (the Codex home directory) at execution time so Codex can discover "$paperclip" and related skills without polluting the project working directory.
 - Unless explicitly overridden in adapter config, Paperclip runs Codex with a per-company managed CODEX_HOME under the active Paperclip instance and seeds auth/config from the shared Codex home (the CODEX_HOME env var, when set, or ~/.codex).
 - Some model/tool combinations reject certain effort levels (for example minimal with web search enabled).
 - When Paperclip realizes a workspace/runtime for a run, it injects PAPERCLIP_WORKSPACE_* and PAPERCLIP_RUNTIME_* env vars for agent-side tooling.

packages/adapters/codex-local/src/server/execute.ts

@@ -21,7 +21,7 @@ import {
   runChildProcess,
 } from "@paperclipai/adapter-utils/server-utils";
 import { parseCodexJsonl, isCodexUnknownSessionError } from "./parse.js";
-import { pathExists, prepareManagedCodexHome, resolveManagedCodexHomeDir } from "./codex-home.js";
+import { pathExists, prepareManagedCodexHome, resolveManagedCodexHomeDir, resolveSharedCodexHomeDir } from "./codex-home.js";
 import { resolveCodexDesiredSkillNames } from "./skills.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
@@ -135,8 +135,8 @@ async function pruneBrokenUnavailablePaperclipSkillSymlinks(
   }
 }
 
-function resolveCodexWorkspaceSkillsDir(cwd: string): string {
+function resolveCodexSkillsHome(): string {
-  return path.join(cwd, ".agents", "skills");
+  return path.join(resolveSharedCodexHomeDir(), "skills");
 }
 
 type EnsureCodexSkillsInjectedOptions = {
@@ -157,7 +157,7 @@ export async function ensureCodexSkillsInjected(
   const skillsEntries = allSkillsEntries.filter((entry) => desiredSet.has(entry.key));
   if (skillsEntries.length === 0) return;
 
-  const skillsHome = options.skillsHome ?? resolveCodexWorkspaceSkillsDir(process.cwd());
+  const skillsHome = options.skillsHome ?? resolveCodexSkillsHome();
   await fs.mkdir(skillsHome, { recursive: true });
   const linkSkill = options.linkSkill;
   for (const entry of skillsEntries) {
@@ -273,11 +273,11 @@ export async function execute(ctx: AdapterExecutionContext): Promise<AdapterExec
   const defaultCodexHome = resolveManagedCodexHomeDir(process.env, agent.companyId);
   const effectiveCodexHome = configuredCodexHome ?? preparedManagedCodexHome ?? defaultCodexHome;
   await fs.mkdir(effectiveCodexHome, { recursive: true });
-  const codexWorkspaceSkillsDir = resolveCodexWorkspaceSkillsDir(cwd);
+  const codexSkillsDir = resolveCodexSkillsHome();
   await ensureCodexSkillsInjected(
     onLog,
     {
-      skillsHome: codexWorkspaceSkillsDir,
+      skillsHome: codexSkillsDir,
       skillsEntries: codexSkillEntries,
       desiredSkillNames,
     },

packages/adapters/codex-local/src/server/skills.ts

@@ -31,7 +31,7 @@ async function buildCodexSkillSnapshot(
     sourcePath: entry.source,
     targetPath: null,
     detail: desiredSet.has(entry.key)
-      ? "Will be linked into the workspace .agents/skills directory on the next run."
+      ? "Will be linked into ~/.codex/skills/ on the next run."
       : null,
     required: Boolean(entry.required),
     requiredReason: entry.requiredReason ?? null,

server/src/__tests__/codex-local-execute.test.ts

@@ -210,7 +210,7 @@ describe("codex execute", () => {
       "company-1",
       "codex-home",
     );
-    const workspaceSkill = path.join(workspace, ".agents", "skills", "paperclip");
+    const homeSkill = path.join(sharedCodexHome, "skills", "paperclip");
     await fs.mkdir(workspace, { recursive: true });
     await fs.mkdir(sharedCodexHome, { recursive: true });
     await fs.writeFile(path.join(sharedCodexHome, "auth.json"), '{"token":"shared"}\n', "utf8");
@@ -284,7 +284,7 @@ describe("codex execute", () => {
       expect(await fs.realpath(isolatedAuth)).toBe(await fs.realpath(path.join(sharedCodexHome, "auth.json")));
       expect((await fs.lstat(isolatedConfig)).isFile()).toBe(true);
       expect(await fs.readFile(isolatedConfig, "utf8")).toBe('model = "codex-mini-latest"\n');
-      expect((await fs.lstat(workspaceSkill)).isSymbolicLink()).toBe(true);
+      expect((await fs.lstat(homeSkill)).isSymbolicLink()).toBe(true);
       expect(logs).toContainEqual(
         expect.objectContaining({
           stream: "stdout",
@@ -371,7 +371,7 @@ describe("codex execute", () => {
 
       const capture = JSON.parse(await fs.readFile(capturePath, "utf8")) as CapturePayload;
       expect(capture.codexHome).toBe(explicitCodexHome);
-      expect((await fs.lstat(path.join(workspace, ".agents", "skills", "paperclip"))).isSymbolicLink()).toBe(true);
+      expect((await fs.lstat(path.join(sharedCodexHome, "skills", "paperclip"))).isSymbolicLink()).toBe(true);
       await expect(fs.lstat(path.join(paperclipHome, "instances", "worktree-1", "codex-home"))).rejects.toThrow();
     } finally {
       if (previousHome === undefined) delete process.env.HOME;

server/src/__tests__/codex-local-skill-sync.test.ts

@@ -43,7 +43,7 @@ describe("codex local skill sync", () => {
     expect(before.desiredSkills).toContain(paperclipKey);
     expect(before.entries.find((entry) => entry.key === paperclipKey)?.required).toBe(true);
     expect(before.entries.find((entry) => entry.key === paperclipKey)?.state).toBe("configured");
-    expect(before.entries.find((entry) => entry.key === paperclipKey)?.detail).toContain(".agents/skills");
+    expect(before.entries.find((entry) => entry.key === paperclipKey)?.detail).toContain("~/.codex/skills/");
   });
 
   it("does not persist Paperclip skills into CODEX_HOME during sync", async () => {